Adding optional properties file for biopet

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala

@@ -30,7 +30,6 @@ import scala.util.Random
 import scala.concurrent.duration._
 import scala.concurrent.{Await, Future}
 import scala.concurrent.ExecutionContext.Implicits.global
-
 import org.apache.spark.SparkContext
 import org.apache.spark.SparkConf
 
@@ -77,8 +76,6 @@ object VcfStats extends ToolCommand {
                                    "Filtered",
                                    "Variant")
 
-  //protected var cmdArgs: Args = _
-
   val defaultGenotypeFields =
     List("DP", "GQ", "AD", "AD-ref", "AD-alt", "AD-used", "AD-not_used", "general")
 
@@ -108,7 +105,7 @@ object VcfStats extends ToolCommand {
     logger.info("Init spark context")
 
     val conf = new SparkConf()
-      .setAppName(this.getClass.getSimpleName)
+      .setAppName(commandName)
       .setMaster(cmdArgs.sparkMaster.getOrElse(s"local[${cmdArgs.localThreads}]"))
     val sparkContext = new SparkContext(conf)
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsSpark.scala

@@ -61,7 +61,7 @@ object VcfStatsSpark extends ToolCommand {
       .getURLs
       .map(_.getFile)
     val conf = new SparkConf()
-      .setAppName(this.getClass.getSimpleName)
+      .setAppName(commandName)
       .setMaster(cmdArgs.sparkMaster.getOrElse(s"local[${cmdArgs.localThreads}]"))
       .setJars(jars)
     val sc = new SparkContext(conf)

biopet-tools/src/test/resources/biopet.properties

+spark.driver.memory=500000000
+spark.testing.memory=500000000

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ToolCommand.scala

@@ -21,6 +21,8 @@ import nl.lumc.sasc.biopet.FullVersion
   */
 trait ToolCommand extends MainCommand with Logging {
 
+  loadBiopetProperties()
+
   protected type Args
   protected type OptParser <: AbstractOptParser[Args]
 }

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala

@@ -114,4 +114,14 @@ package object utils {
       case _ => a.toString < b.toString
     }
   }
+
+  def loadBiopetProperties(): Unit = {
+    val is = getClass.getClassLoader.getResourceAsStream("biopet.properties")
+    if (is != null) {
+      val prop = System.getProperties
+      prop.load(is)
+      System.setProperties(prop)
+    }
+
+  }
 }